Accelerating BLAST Computation on an FPGA-enhanced PC Cluster

This paper introduces an FPGA-based scheme to accelerate mpiBLAST, which is a parallel sequence alignment algorithm for computational biology. Recent rapidly growing biological databases for sequence alignment require highthroughput storage and network rather than computing speed. Our scheme utilizes a specialized hardware configured on an FPGA-board which connects flash storage and other FPGAboards directly. The specialized hardware configured on the FPGAs, we call a Data Stream Processing Engine (DSPE), take a role for preprocessing to adjust data for high-performance multi- and many- core processors simultaneously with offloading system-calls for storage access and networking. DSPE along the datapath achieves in-datapath computing which applies operations for data streams passing through the FPGA. Two functions in mpiBLAST are implemented using DSPE to offload operations along the datapath. The first function is database partitioning, which distributes the biological database to multiple computing nodes before commencing the BLAST processes. Using DSPE, we observe a 20-fold improvement in computation time for the database partitioning operation. The second function is an early part of the BLAST process that determines the positions of sequences for more detailed computations. We implement IDP-BLAST (In-datapath BLAST), which annotates positions in data streams from solid-state drives. We show that IDP-BLAST accelerates the computation time of the preprocess of BLAST by a factor of three hundred by offloading heavy operations to the introduced special hardware

Sharing Computing Resources with Virtual Machines by Transparent Data Access

Cloud computing has rapid growth in enterprise and academic areas. Computing platform makes up the transition from physical servers to virtual machines (VMs) in the cloud. Instead of many advantages, VMs remain several problems to employ effective utilization of physical computing resources, especially many-core accelerators. Even though GPGPU is a hopeful solution for high-load applications, existing methods to utilize GPUs from VMs are subjected to various restraints. In order to solve this problem, we propose a flexible method to share external computing resources by providing transparent access for data in the VMs. By committing commands to a computing host which processes the jobs as substitution, VMs can process high load jobs as necessary even if the VM has a tiny configuration. The computing host mounts the working directories in the VMs and enqueues jobs committed by the VMs. Experimental results show that the overhead of our implementation is sufficiently small in the low I/O load processes

A Light-weight Content Distribution Scheme for Cooperative Caching in Telco-CDNs

A key technique to reduce the rapid growing of video-on-demand’s traffic is a cooperative caching strategy aggregating multiple cache storages. Many internet service providers have considered the use of cache servers on their networks as a solution to reduce the traffic. Existing schemes often periodically calculate a sub-optimal allocation of the content caches in the network. However, such approaches require a large computational overhead that cannot be amortized in a presence of frequent changes of the contents’ popularities. This paper proposes a light-weight scheme for a cooperative caching that obtains a sub-optimal distribution of the contents by focusing on their popularities. This was made possible by adding color tags to both cache servers and contents. In addition, we propose a hybrid caching strategy based on Least Frequently Used (LFU) and Least Recently Used (LRU) schemes, which efficiently manages the contents even with a frequent change in the popularity. Evaluation results showed that our light-weight scheme could considerably reduce the traffic, reaching a sub-optimal result. In addition, the performance gain is obtained with a computation overhead of just a few seconds. The evaluation results also showed that the hybrid caching strategy could follow the rapid variation of the popularity. While a single LFU strategy drops the hit ratio by 13.9%, affected by rapid popularity changes, our proposed hybrid strategy could limit the degradation to only 2.3%

The Relationship between the Efficacy of Tonsillectomy and Renal Pathology in the Patients with IgA Nephropathy

Objective. The aim of this study was to evaluate the effects of tonsillectomy as a treatment for IgA nephropathy in relation to renal pathological findings. Methods. This is a retrospective analysis of 13 patients having IgA nephropathy treated by tonsillectomy. Results. UP/UCre levels decreased from 820.8 to 585.4 one month postsurgery and then showed slight worsening to 637.3 at the most recent follow-up. There was no significant difference in the improvement rate between pathological grades I–III and IV. There was positive correlation between Pre-UP/UCre level and the reduction rate of UP/UCre, which was statistically significant (R = 0.667, R2 = 0.445, and P=0.01). Conclusions. Reduction of UP/UCre at one month postsurgery is considered to be an overall prognostic factor, and tonsillectomy is considered to be an effective therapy for IgA patients regardless of the grade of renal pathology

Examination of Wireless Power Transfer Combined With the Utilization of Distance Detection

Wireless power transfer using magnetic resonant coupling is expected to be widely used in the charging of an electric vehicle and in the use of home electric appliances. Wireless power transfer requires a high efficiency and power transfer over a long distance. However, the efficiency is reduced by the increase of the transmission distance and the change of the impedance of the receiving load. Therefore, a distance sensor using magnetic resonant coupling is proposed. In this paper, we propose a method of power transfer and distance detection using one couple of coils in real time. We also propose to use different frequencies in the power transfer and the distance detection, which are superposed and separated. Using the proposed approach, we demonstrated that the power transfer and the distance detection can be performed without relying on the change of the transmission distance.ArticleIEEE TRANSACTIONS ON MAGNETICS. 50(11):4005304 (2014)journal articl

Wire-Speed Implementation of Sliding-Window Aggregate Operator over Out-of-Order Data Streams

This paper shows the design and evaluation of an FPGA-based accelerator for sliding-window aggregation over data streams with out-of-order data arrival. We propose an order-agnostic hardware implementation technique for windowing operators based on a one-pass query evaluation strategy called Window-ID, which is originally proposed for software implementation. The proposed implementation succeeds to process out-of-order data items, or tuples, at wire speed due to the simultaneous evaluations of overlapping sliding-windows. In order to verify the effectiveness of the proposed approach, we have also implemented an experimental system as a case study. Our experiments demonstrate that the proposed accelerator with a network interface achieves an effective throughput around 760 Mbps or equivalently nearly 6 million tuples per second, by fully utilizing the available bandwidth of the network interface

Examination of Wireless Power Transfer Combined With the Utilization of Distance Detection

Wireless power transfer using magnetic resonant coupling is expected to be widely used in the charging of an electric vehicle and in the use of home electric appliances. Wireless power transfer requires a high efficiency and power transfer over a long distance. However, the efficiency is reduced by the increase of the transmission distance and the change of the impedance of the receiving load. Therefore, a distance sensor using magnetic resonant coupling is proposed. In this paper, we propose a method of power transfer and distance detection using one couple of coils in real time. We also propose to use different frequencies in the power transfer and the distance detection, which are superposed and separated. Using the proposed approach, we demonstrated that the power transfer and the distance detection can be performed without relying on the change of the transmission distance.ArticleIEEE TRANSACTIONS ON MAGNETICS. 50(11):4005304 (2014)journal articl

Inhibition of cell movement and proliferation by cell–cell contact-induced interaction of Necl-5 with nectin-3

Immunoglobulin-like Necl-5/Tage4/poliovirus receptor (PVR)/CD155, originally identified as the PVR, has been shown to be up-regulated in cancer cells and to enhance growth factor–induced cell movement and proliferation. In addition, Necl-5 heterophilically trans-interacts with nectin-3, a cell–cell adhesion molecule known to form adherens junctions in cooperation with cadherin. We show here that Necl-5 was down-regulated from cell surface upon cell–cell contacts in NIH3T3 cells. This down-regulation of Necl-5 was initiated by its interaction with nectin-3 and was mainly mediated by clathrin-dependent endocytosis. Then, the down-regulation of Necl-5 induced in this way reduced movement and proliferation of NIH3T3 cells. These results indicate that the down-regulation of Necl-5 induced by its interaction with nectin-3 upon cell–cell contacts may be at least one mechanism underlying contact inhibition of cell movement and proliferation

An Efficient and Scalable Implementation of Sliding-Window Aggregate Operator on FPGA

This paper presents an efficient and scalable implementation of an FPGA-based accelerator for sliding-window aggregates over disordered data streams. With an increasing number of overlapping sliding-windows, the window aggregates have a serious scalability issue, especially when it comes to implementing them in parallel processing hardware (e.g., FPGAs). To address the issue, we propose a resource-ef?cient, scalable, and order-agnostic hardware design and its implementation by examining and integrating two key concepts, called Window-ID and Pane, which are originally proposed for software implementation, respectively. Evaluation results show that the proposed implementation scales well compared to the previous FPGA implementation in terms of both resource consumption and performance. The proposed design is fully pipelined and our implementation can process out-of-order data items, or tuples, at wire speed up to 200 million tuples per second

Versican provides the provisional matrix for uterine spiral artery dilation and fetal growth

The extracellular matrix (ECM) in the endometrium plays a crucial role in mammalian pregnancy. We have shown that versican secreted from the endometrial epithelium promotes embryo implantation. Versican is a proteoglycan, a major player in the provisional matrix, and versikine, its N-terminal fragment cleaved by ADAMTS proteinases, serves as a bioactive molecule. Here, since versican expression in the placenta was dynamically altered in humans and mice, we investigated the role of versican in pregnancy using uterine-specific Vcan deletion mice (uKO mice) and ADAMTS-resistant versican expressing mice (V1R mice). uKO mice exhibited insufficient spiral artery dilation, followed by fetal growth restriction and maternal hypertension. Further analysis revealed impaired proliferation of tissue-resident natural killer cells required for spiral artery dilation. V1R mice showed the same results as the control, eliminating the involvement of versikine. Our results provide a new concept that versican, one factor of ECM, contributes to placentation and following fetal growth